[gpaw-users] BSSE parallel issue

[Glen Jenness]

Hi GPAW users!
I ran into a curious problem when running GPAW in parallel while specifying
ghost centers for a BSSE correction.

I will be able to run my dimer system (in this case a CO molecule on a Rh
(111) surface), but then when I specify calc.set(setups={'Rh': 'ghost"
etc.), it'll enter the memory estimate part, and then freeze if I run over
1 node.

A colleague suggested setting the parallel option sl_auto to True, but
doing so gives:

] [27] gpaw-python(PyObject_Call+0x5d) [0x49128d]
[compute-0-6:29024] [28] gpaw-python(PyEval_EvalFrameEx+0x399d) [0x50dbfd]
[compute-0-6:29024] [29] gpaw-python(PyEval_EvalCodeEx+0x89b) [0x511ffb]
[compute-0-6:29024] *** End of error message ***
[compute-0-9.local:17479] [0,0,0] ORTE_ERROR_LOG: Timeout in file
base/pls_base_orted_cmds.c at line 275
[compute-0-9.local:17479] [0,0,0] ORTE_ERROR_LOG: Timeout in file
pls_tm_module.c at line 572
[compute-0-9.local:17479] [0,0,0] ORTE_ERROR_LOG: Timeout in file
errmgr_hnp.c at line 90
mpirun noticed that job rank 0 with PID 17481 on node compute-0-9 exited on
signal 11 (Segmentation fault).
[compute-0-9.local:17479] [0,0,0] ORTE_ERROR_LOG: Timeout in file
base/pls_base_orted_cmds.c at line 188
[compute-0-9.local:17479] [0,0,0] ORTE_ERROR_LOG: Timeout in file
pls_tm_module.c at line 603


Any idea what could cause either issue?

Thanks!

My python input is:

from ase.atoms import Atoms
from ase.lattice.surface import fcc111, add_adsorbate
from ase.constraints import FixAtoms
from ase.optimize.lbfgs import LBFGS
from ase.parallel import parprint

from gpaw import GPAW, Mixer, FermiDirac

PL = {'sl_auto': True}

verb = False
mix = Mixer(beta=0.40, nmaxold=45, weight=50.0)
occ = FermiDirac(0.1)

calc = GPAW(mode='lcao', basis='dzp', txt='rhodium.txt', kpts=(5,5,1),
occupations=occ, xc='PBE', verbose=verb, mixer=mix, parallel=PL)

rhodium = fcc111('Rh', (1,1,4), vacuum=8.0)
constraint = FixAtoms([0, 1])
rhodium.set_constraint(constraint)
rhodium *= (2,2,1)

co = Atoms('CO', positions=[(0,0,0), (0,0,1.14)])
add_adsorbate(rhodium, co, 1.8, position='ontop')

rhodium.set_calculator(calc)

opt = LBFGS(rhodium, trajectory='co-rhodium.traj')
opt.run(fmax=0.01)
e_ads = rhodium.get_potential_energy()
parprint('e_ads = %f' % e_ads)

calc.set(setups={'Rh': 'ghost', 'C': 'paw', 'O': 'paw'})
rhodium.set_calculator(calc)
e_co = rhodium.get_potential_energy()
parprint('e_co = %s' % e_co)

calc.set(setups={'Rh': 'paw', 'C': 'ghost', 'O': 'ghost'})
rhodium.set_calculator(calc)
e_surf = rhodium.get_potential_energy()
parprint('e_surf = %s' % e_surf)

parprint('E_BE = %f' % ( e_ads - e_co - e_surf))

-- 
Dr. Glen Jenness
Schmidt Group/Morgan Group
Department of Chemistry/Materials Science and Engineering (MSAE)
University of Wisconsin - Madison
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